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Egyptian protesters chant slogans against the country's ruling military council and presidential candidate Ahmed Shafiq in Tahrir Square in Cairo, Friday, June 15. Judges appointed by Hosni Mubarak dissolved the Islamist-dominated parliament Thursday and ruled that Mubarak's former prime minister can stand in the presidential runoff this weekend, setting the stage for the military and remnants of the old regime to stay in power.

With the decision to dissolve parliament yesterday, Egypt's Constitutional Court did more than send a message to 30 million citizens that their votes don't count. It concentrated even more power in the hands of the military junta that has run the Arab world's largest country for 18 months and counting.

In so doing, the wildest hopes of the revolutionary activists and average citizens who poured into the streets of Cairo and a dozen other cities in January and February of 2011 have been dashed. Former Gen. Hosni Mubarak may have been forced out by the protests, but the military establishment and the tools of political repression that Egyptian state apparatus have wielded so effectively since the 1950s remained in place.

Egypt's transition, such as it is, continues to lurch on. But any hope of a fundamental change – of a military subordinated to civilian control, an end to indefinite detention of political activists by security agencies, a reset of a sclerotic and corrupt government bureaucracy – has been dashed, at least for now.

Nathan Brown of George Washington University had a sharp, grim assessment of what he termed "Cairo's Judicial Coup" yesterday: "The [Supreme Constitutional Court's] actions today, occurring in the context that they do, reshape Egypt's transition process – so much so that some Egyptians will likely wonder if they are in any 'transition process' at all. That concern is justified. The 'process' part was already dead. Now the 'transition' part is dying."

Perhaps high hopes were always naive. Mubarak, after all, was not a supreme dictator. He was merely the man at the top of a pyramid of military businesses, fiefdoms carved out by retired generals and their cronies, and a national order designed to make the average Egyptian more subject than citizen. Yesterday's decision to dissolve parliament was made by a "Constitutional" court appointed by Mubarak that operates under a set of constitutional decrees issued by senior officers, who were also appointed by Mubarak. Only the thinnest veneer of checks and balances has been thrown over the process.

What is Egypt's governing document at the moment? A constitutional declaration issued by the generals in March. Article 58 of that document is perhaps the most salient. It begins: "The Supreme Council of the Armed Forces [SCAF] runs the affairs of the State." It goes on to say that SCAF controls legislation, the budget, the cabinet, and foreign affairs. In other words, everything.

In the past 24 hours the junta dispatched riot police across the capital to head off protests, though there has as yet been no sign of major mobilizations like those that swept Egypt early last year. The country's economy, fragile to begin with, has plummeted in over a year of turmoil. Egyptians are tired, and struggling.

Do they still want democracy? Yes. In a Pew poll released in May, 67 percent of Egyptians said "democracy is preferable to any other kind of government." But their priorities indicate a mass return to the streets over the military's meddling in the political process is unlikely. An improved economy was ranked most important by Egyptians, followed in order by a "fair judiciary," "uncensored media," and "law and order." Free and fair elections came in sixth on that list, and the lowest priority to the Egyptians polled was civilian control of the military.

The country now turns toward a presidential election tomorrow in which the military's choice, Ahmed Shafiq, squares off against the Muslim Brotherhood's Mohamed Morsi. Mr. Shafiq, an air force officer who served in Mubarak's cabinet for years and was appointed his prime minister as part of his last ditch effort to cling to power, was one of the big winners on Thursday. The same court that dissolved parliament ruled THAT a law seeking to disqualify senior Mubarak officials like Shafiq from holding the presidency was unconstitutional. Shortly thereafter, Shafiq delivered what sounded like a victory speech to a cheering crowd shouting "President Shafiq" in Cairo. He barely mentioned the fact that parliament, the only body in Egypt with a shred of democratic legitimacy, had been removed from the scene.

The Brotherhood were the big winners in the parliamentary election, winning half of the seats. That record has now been wiped clean. Mr. Morsi, and his Islamist organization that has struggled against the military for decades, may still grab the brass ring tomorrow, but it's hard to see Egyptian army commander Mohamed Hussein Tantawi and his fellow officers bowing down to kiss it. Morsi was measured in his comments yesterday. While former Muslim Broterhood official Abdel Moneim Aboul Fotouh complained of a "coup," Morsi urged his followers to abide by the court's decision. At any rate, there can be no coup without a change of power. The military's control has only been reasserted, not lost.

But denying the fruits of the ballot box to popular forces in any society is a dangerous one, and the history of elections overturned against Islamists in the Arab world is grim. The Algerian military's nullification of elections in 1991, when Islamists looked set to win, touched off a decade of civil war that claimed hundreds of thousands of lives and spawned virulent jihadi terrorist groups.

While that particular outcome is vanishingly unlikely in Egypt at the moment, Islamist groups have been sent a message that the ballot box is not, in fact, their road to success. While the Brotherhood renounced violence in pursuit of its goals over 40 years ago, smaller militant Egyptian groups have also come in from the cold in recent years. The reactionary salafi sect came in second in the polls, and a young generation of Islamist activists with no memory of how militant groups were crushed in Egypt in the past have just been delivered a punch to the gut. A return to the terrorism that plagued Egypt in the '80s and '90s has just become more likely.

Did the court do the technically right thing? Perhaps. The law on disqualifying senior officials was broad and vaguely written. The parliamentary election was run under a byzantine set of rules that reserved two thirds of the seats for political parties, and one third for "independent" candidates. Ahead of the election, electoral officials allowed politicians affiliated with parties to run as independents. Shafiq was also allowed to run in the first round of the presidential election (the vote tomorrow is a run-off) without a ruling being made on the constitutionality of the law seeking to disqualify him.

As a practical matter, these questions should have been decided before Egyptian's went to the polls – not after, or mid-stride. The political effect of the decisions has been to spread more confusion, and disillusion. It's a basic rule of political transitions that the sooner military rulers are removed from the scene, the better the chances of fundamental change. Egypt's junta originally promised to be out of the governing business by October 2011.

The new Egyptian parliament had little power in practice, with a set of extra-constitutional rules written by the SCAF, hanging over them. But the legislature at least represented something new in Egyptian politics: A body freely chosen by the Egyptian people. That, at least, gave it some moral heft and a potential bully pulpit in dealing with the generals and the winner of the presidency.

Sitting generals have manipulated Egyptian politics, either overtly or in powerful ways behind the scenes, since Lt. Anwar Sadat was dispatched to inform the world of the Free Officer's Coup in 1952. The officer's Revolutionary Command Council made Gamal Abdul Nasser president, and when he passed in 1970, it was military men who decided that Mr. Sadat, Nasser's vice president, would be allowed to succeed him.

But before he was allowed to take the reins (never mind that was the formal legal solution), the senior generals demanded Sadat agree to a set of conditions that would protect the Egyptian military from civilian control. Sadat agreed to give the senior generals then running the Arab Socialist Union a voice in all major initiatives, effective veto power over major initiatives. Only then, was he allowed to take power.

Egypt's next president is almost certain to be presented some version of those demands. Already, the generals sought to impose a set of principals on civilian politicians that would leave their empires beyond the reach of elected officials.

Is all lost? No. Egypt is poor, and struggling. But you only have to look at Iraq after Saddam Hussein was removed from power in 2003, or Syria today, to see what a truly horrific transition looks like. Wisdom and compromise may yet prevail. But those qualities have been tragically absent until now.